| 1. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 2. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 3. |
- Kõljalg, Urmas, et al.
(författare)
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UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
- 2005
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 166:3, s. 1063-1068
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Tidskriftsartikel (refereegranskat)abstract
- Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee.
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| 4. |
- Ekblad, Alf, 1957-, et al.
(författare)
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The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils : role in carbon cycling
- 2013
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 366:1-2, s. 1-27
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Forskningsöversikt (refereegranskat)abstract
- There is growing evidence of the importance of extramatrical mycelium (EMM) of mycorrhizal fungi in carbon (C) cycling in ecosystems. However, our understanding has until recently been mainly based on laboratory experiments, and knowledge of such basic parameters as variations in mycelial production, standing biomass and turnover as well as the regulatory mechanisms behind such variations in forest soils is limited. Presently, the production of EMM by ectomycorrhizal (EM) fungi has been estimated at similar to 140 different forest sites to be up to several hundreds of kg per ha per year, but the published data are biased towards Picea abies in Scandinavia. Little is known about the standing biomass and turnover of EMM in other systems, and its influence on the C stored or lost from soils. Here, focussing on ectomycorrhizas, we discuss the factors that regulate the production and turnover of EMM and its role in soil C dynamics, identifying important gaps in this knowledge. C availability seems to be the key factor determining EMM production and possibly its standing biomass in forests but direct effects of mineral nutrient availability on the EMM can be important. There is great uncertainty about the rate of turnover of EMM. There is increasing evidence that residues of EM fungi play a major role in the formation of stable N and C in SOM, which highlights the need to include mycorrhizal effects in models of global soil C stores.
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| 5. |
- Nielsen, K B, et al.
(författare)
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Colonisation and molecular diversity of arbuscular mycorrhizal fungi in the aquatic plants Littorella uniflora and Lobelia dortmanna in southern Sweden
- 2004
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Ingår i: Mycological Research. - 0953-7562. ; 108:6, s. 616-625
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Tidskriftsartikel (refereegranskat)abstract
- The colonisation intensity and composition of the mycorrhizal community in the aquatic plants Lobelia dortmanna and Littorella uniflora were studied. The mycorrhizal fungi were characterised by fungal specific nested PCR and sequencing using the 5'-end of the LSU rDNA as target. For this, primers for the clade of Acaulospora, the clade including Glomus mosseae and G. intraradices and the clade containing G. etunicatum and G. claroideum were used. The nested PCR products were screened for different sequence types using single stranded conformation polymorphism (SSCP) and representatives for each type were sequenced. A phylogenctic analysis of the sequences showed two phylotypes of Acaulospora, one phylotype within the clade of G. etunicatum/G. claroideum and five within the G. mosseael G. intraradices clade. The colonisation intensity was comparable to that seen in typical grassland vegetation. The neutral lipid fatty acid 16: 1omega5 was seen to be indicative of mycorrhizal colonisation with concentrations up to 35 nmol mg(-1) root DW, which indicates that the fungi are active.
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| 6. |
- Sharma, T., et al.
(författare)
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Biomarkers associated with vulnerable plaques
- 2022
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Ingår i: European Heart Journal. - : Oxford University Press. - 0195-668X .- 1522-9645. ; 43:Suppl. 2, s. 1292-1292
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Background: Cardiovascular heart disease is the leading cause of mortality worldwide, with the rupture or thrombosis of an atherosclerotic plaque being the main reason behind an acute coronary syndrome. It has already been established that the morphology of atherosclerotic plaques determine their stability. A lipid rich lesion with a thin fibrous cap is more prone to rupture compared to solid fibrous lesions. In the PROSPECTII study we used Near infrared spectroscopy (NIRS) and Intravascular ultrasound (IVUS) to identify atherosclerotic plaques in the coronary arteries; NIRS-derived lipid core burden index (LCBI) and IVUS-derived plaque burden (PB) identified plaques that caused adverse cardiovascular events.Purpose: Our aim is to find biomarkers associated with LCBI or PB, to understand the development of vulnerable plaques.Methods: 902 patients were enrolled in this study after successful percutaneous coronary intervention (PCI). A combined NIRS-IVUS catheter was then used to analyze approximately 200m of coronary arteries. Blood samples for biomarker analysis were taken before the PCI procedure and plasma levels of 182 proteins associated with cardiovascular disease were assessed using a novel method for measuring proximity extension assay. Adjusted linear regression models were calculated between the biomarkers and the outcomes of interest, followed by a false discovery rate (FDR) correction.Results: We found 24 proteins associated with plaque burden and 28 proteins associated with LCBI after using a cut off of two tailed P value <0.05. An overlap of 8 biomarkers could be seen between the two groups. After adjusting the P values with FDR, Angiopoeitin like 3 (ANGPTL3) retain edits association to LCBI, and Interleukin 18 receptor 1 (IL18R1) and colony stimulating factor 1 (CSF-1) to plaque burden.Conclusion: We were able to identify different biomarker patterns associated with plaque burden compared to lipid rich vulnerable plaques. ANGPTL3 was shown to only have an association with lipid rich plaques and not with solid fibrous lesions which further supports its role in vulnerable plaques.
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| 7. |
- Wallander, Håkan, et al.
(författare)
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Evaluation of methods to estimate production, biomass and turnover of ectomycorrhizal mycelium in forests soils : a review
- 2013
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 57, s. 1034-1047
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Forskningsöversikt (refereegranskat)abstract
- Mycorrhizal fungi constitute a considerable sink for carbon in most ecosystems. This carbon is used for building extensive mycelial networks in the soil as well as for metabolic activity related to nutrient uptake. A number of methods have been developed recently to quantify production, standing biomass and turnover of extramatrical mycorrhizal mycelia (EMM) in the field. These methods include minirhizotrons, in-growth mesh bags and cores, and indirect measurements of EMM based on classification of ectomycorrhizal fungi into exploration types. Here we review the state of the art of this methodology and discuss how it can be developed and applied most effectively in the field, Furthermore, we also discuss different ways to quantify fungal biomass based on biomarkers such as chitin, ergosterol and PLFAs, as well as molecular methods, such as qPCR. The evidence thus far indicates that mycorrhizal fungi are key components of microbial biomass in many ecosystems. We highlight the need to extend the application of current methods to focus on a greater range of habitats and mycorrhizal types enabling incorporation of mycorrhizal fungal biomass and turnover into biogeochemical cycling models.
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